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Dey D, Dasgupta A, Ghosh D, Bhattacharjee O, Ghosh A, Honda A, Chattopadhyay D. Host proteins Alpha-2-Macroglobulin and LRP1 associate with Chandipura virus. Biochimie 2024; 218:105-117. [PMID: 37517577 DOI: 10.1016/j.biochi.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Chandipura Virus is an emerging tropical pathogen with a high mortality rate among children. No mode of treatment or antivirals exists against CHPV infection, due to little information regarding its host interaction. Studying viral pathogen interaction with its host can not only provide valuable information regarding its propagation strategy, but also on which host proteins interact with the virus. Identifying these proteins and understanding their role in the infection process can provide more stable anti-viral targets. In this study, we focused on identifying host factors that interact with CHPV and may play a critical role in CHPV infection. We are the first to report the successful identification of Alpha-2-Macroglobulin (A2M), a secretory protein of the host that interacts with CHPV. We also established that LRP1 (Low-density lipoprotein receptor-related protein 1) and GRP78 (Glucose regulated protein 78), receptors of A2M, also interact with CHPV. Furthermore, we could also demonstrate that knocking out A2M has a severe effect on viral infection. We conclusively show the interaction of these host proteins with CHPV. Our findings also indicate that these host proteins could play a role in viral entry into the host cell.
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Affiliation(s)
- Dhritiman Dey
- Department of Biotechnology, University of Calcutta, Kolkata, India
| | | | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, India
| | | | - Abhrajyoti Ghosh
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Ayae Honda
- Tokyo University of Agriculture and Technology, Tokyo, Japan
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2
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Abad P, Coronado M, Vincelle-Nieto Á, Pérez-Benavente S, Fobil JN, Puyet A, Diez A, Reyes-Palomares A, Azcárate IG, Bautista JM. Shotgun Characterization of the Circulating IgM Antigenome of an Infectious Pathogen by Immunocapture-LC-MS/MS from Dried Serum Spots. J Proteome Res 2024; 23:633-643. [PMID: 38183416 DOI: 10.1021/acs.jproteome.3c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
One of the main challenges in compiling the complete collection of protein antigens from pathogens for the selection of vaccine candidates or intervention targets is to acquire a broad enough representation of them to be recognized by the highly diversified immunoglobulin repertoire in human populations. Dried serum spot sampling (DSS) retains a large repertoire of circulating immunoglobulins from each individual that can be representative of a population, according to the sample size. In this work, shotgun proteomics of an infectious pathogen based on DSS sampling coupled with IgM immunoprecipitation, liquid chromatography-mass spectrometry (LC-MS/MS), and bioinformatic analyses was combined to characterize the circulating IgM antigenome. Serum samples from a malaria endemic region at different clinical statuses were studied to optimize IgM binding efficiency and antibody leaching by varying serum/immunomagnetic bead ratios and elution conditions. The method was validated using Plasmodium falciparum extracts identifying 110 of its IgM-reactive antigens while minimizing the presence of human proteins and antibodies. Furthermore, the IgM antigen recognition profile differentiated between malaria-infected and noninfected individuals at the time of sampling. We conclude that a shotgun proteomics approach offers advantages in providing a high-throughput, reliable, and clean way to identify IgM-recognized antigens from trace amounts of serum. The mass spectrometry raw data and metadata have been deposited with ProteomeXchange via MassIVE with the PXD identifier PXD043800.
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Affiliation(s)
- Paloma Abad
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
| | - Montserrat Coronado
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
| | - África Vincelle-Nieto
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
| | - Susana Pérez-Benavente
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
| | - Julius N Fobil
- Department of Biological, Environmental & Occupational Health Sciences, School of Public Health, College of Health Sciences, University of Ghana, P.O. Box LG 13, G-4381 Legon, Ghana
| | - Antonio Puyet
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
- 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain
| | - Amalia Diez
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
- 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain
| | - Armando Reyes-Palomares
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
- 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain
| | - Isabel G Azcárate
- Faculty of Health Sciences, Rey Juan Carlos University, Alcorcón, 28922 Madrid, Spain
| | - José M Bautista
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Faculty of Veterinary Sciences, 28040 Madrid, Spain
- 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain
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3
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Vital T, Wali A, Butler KV, Xiong Y, Foster JP, Marcel SS, McFadden AW, Nguyen VU, Bailey BM, Lamb KN, James LI, Frye SV, Mosely AL, Jin J, Pattenden SG, Davis IJ. MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing. Front Oncol 2023; 13:1099550. [PMID: 36793594 PMCID: PMC9924231 DOI: 10.3389/fonc.2023.1099550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.
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Affiliation(s)
- Tamara Vital
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Aminah Wali
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kyle V. Butler
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joseph P. Foster
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shelsa S. Marcel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andrew W. McFadden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Valerie U. Nguyen
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benton M. Bailey
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lindsey I. James
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stephen V. Frye
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amber L. Mosely
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Samantha G. Pattenden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ian J. Davis
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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4
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Spectrin-beta 2 facilitates the selective accumulation of GABA A receptors at somatodendritic synapses. Commun Biol 2023; 6:11. [PMID: 36604600 PMCID: PMC9816108 DOI: 10.1038/s42003-022-04381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
Fast synaptic inhibition is dependent on targeting specific GABAAR subtypes to dendritic and axon initial segment (AIS) synapses. Synaptic GABAARs are typically assembled from α1-3, β and γ subunits. Here, we isolate distinct GABAARs from the brain and interrogate their composition using quantitative proteomics. We show that α2-containing receptors co-assemble with α1 subunits, whereas α1 receptors can form GABAARs with α1 as the sole α subunit. We demonstrate that α1 and α2 subunit-containing receptors co-purify with distinct spectrin isoforms; cytoskeletal proteins that link transmembrane proteins to the cytoskeleton. β2-spectrin was preferentially associated with α1-containing GABAARs at dendritic synapses, while β4-spectrin was associated with α2-containing GABAARs at AIS synapses. Ablating β2-spectrin expression reduced dendritic and AIS synapses containing α1 but increased the number of synapses containing α2, which altered phasic inhibition. Thus, we demonstrate a role for spectrins in the synapse-specific targeting of GABAARs, determining the efficacy of fast neuronal inhibition.
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5
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Choi C, Smalley JL, Lemons AHS, Ren Q, Bope CE, Dengler JS, Davies PA, Moss SJ. Analyzing the mechanisms that facilitate the subtype-specific assembly of γ-aminobutyric acid type A receptors. Front Mol Neurosci 2022; 15:1017404. [PMID: 36263376 PMCID: PMC9574402 DOI: 10.3389/fnmol.2022.1017404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/07/2022] [Indexed: 01/16/2023] Open
Abstract
Impaired inhibitory signaling underlies the pathophysiology of many neuropsychiatric and neurodevelopmental disorders including autism spectrum disorders and epilepsy. Neuronal inhibition is regulated by synaptic and extrasynaptic γ-aminobutyric acid type A receptors (GABA A Rs), which mediate phasic and tonic inhibition, respectively. These two GABA A R subtypes differ in their function, ligand sensitivity, and physiological properties. Importantly, they contain different α subunit isoforms: synaptic GABA A Rs contain the α1-3 subunits whereas extrasynaptic GABA A Rs contain the α4-6 subunits. While the subunit composition is critical for the distinct roles of synaptic and extrasynaptic GABA A R subtypes in inhibition, the molecular mechanism of the subtype-specific assembly has not been elucidated. To address this issue, we purified endogenous α1- and α4-containing GABA A Rs from adult murine forebrains and examined their subunit composition and interacting proteins using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and quantitative analysis. We found that the α1 and α4 subunits form separate populations of GABA A Rs and interact with distinct sets of binding proteins. We also discovered that the β3 subunit, which co-purifies with both the α1 and α4 subunits, has different levels of phosphorylation on serines 408 and 409 (S408/9) between the two receptor subtypes. To understand the role S408/9 plays in the assembly of α1- and α4-containing GABA A Rs, we examined the effects of S408/9A (alanine) knock-in mutation on the subunit composition of the two receptor subtypes using LC-MS/MS and quantitative analysis. We discovered that the S408/9A mutation results in the formation of novel α1α4-containing GABA A Rs. Moreover, in S408/9A mutants, the plasma membrane expression of the α4 subunit is increased whereas its retention in the endoplasmic reticulum is reduced. These findings suggest that S408/9 play a critical role in determining the subtype-specific assembly of GABA A Rs, and thus the efficacy of neuronal inhibition.
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Affiliation(s)
- Catherine Choi
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Joshua L. Smalley
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Abigail H. S. Lemons
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Qiu Ren
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Christopher E. Bope
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Jake S. Dengler
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Paul A. Davies
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Stephen J. Moss
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States,Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom,*Correspondence: Stephen J. Moss,
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6
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Reboll MR, Klede S, Taft MH, Cai CL, Field LJ, Lavine KJ, Koenig AL, Fleischauer J, Meyer J, Schambach A, Niessen HW, Kosanke M, van den Heuvel J, Pich A, Bauersachs J, Wu X, Zheng L, Wang Y, Korf-Klingebiel M, Polten F, Wollert KC. Meteorin-like promotes heart repair through endothelial KIT receptor tyrosine kinase. Science 2022; 376:1343-1347. [PMID: 35709278 PMCID: PMC9838878 DOI: 10.1126/science.abn3027] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Effective tissue repair after myocardial infarction entails a vigorous angiogenic response, guided by incompletely defined immune cell-endothelial cell interactions. We identify the monocyte- and macrophage-derived cytokine METRNL (meteorin-like) as a driver of postinfarction angiogenesis and high-affinity ligand for the stem cell factor receptor KIT (KIT receptor tyrosine kinase). METRNL mediated angiogenic effects in cultured human endothelial cells through KIT-dependent signaling pathways. In a mouse model of myocardial infarction, METRNL promoted infarct repair by selectively expanding the KIT-expressing endothelial cell population in the infarct border zone. Metrnl-deficient mice failed to mount this KIT-dependent angiogenic response and developed severe postinfarction heart failure. Our data establish METRNL as a KIT receptor ligand in the context of ischemic tissue repair.
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Affiliation(s)
- Marc R. Reboll
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Stefanie Klede
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Manuel H. Taft
- Institute for Biophysical Chemistry, Hannover Medical School; 30625 Hannover, Germany
| | - Chen-Leng Cai
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine; Indianapolis, IN 46202, USA
| | - Loren J. Field
- Krannert Cardiovascular Research Center and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine; Indianapolis, IN 46202, USA
| | - Kory J. Lavine
- Center for Cardiovascular Research, Department of Medicine, Washington University School of Medicine; St. Louis, MO 63110, USA
| | - Andrew L. Koenig
- Center for Cardiovascular Research, Department of Medicine, Washington University School of Medicine; St. Louis, MO 63110, USA
| | - Jenni Fleischauer
- Institute of Experimental Hematology, Hannover Medical School; 30625 Hannover, Germany
| | - Johann Meyer
- Institute of Experimental Hematology, Hannover Medical School; 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School; 30625 Hannover, Germany
| | - Hans W. Niessen
- Department of Pathology and Department of Cardiac Surgery, Institute for Cardiovascular Research, University Medical Center; 1007 MB Amsterdam, The Netherlands
| | - Maike Kosanke
- Research Core Unit Genomics, Hannover Medical School; 30625 Hannover, Germany
| | - Joop van den Heuvel
- Technology Platform Recombinant Protein Expression, Helmholtz Center for Infection Research; 38124 Braunschweig, Germany
| | - Andreas Pich
- Core Unit Proteomics and Institute of Toxicology, Hannover Medical School; 30625 Hannover, Germany
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Xuekun Wu
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Linqun Zheng
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Yong Wang
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Mortimer Korf-Klingebiel
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Felix Polten
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
| | - Kai C. Wollert
- Division of Molecular and Translational Cardiology, Hans Borst Center for Heart and Stem Cell Research, Hannover Medical School; 30625 Hannover, Germany
- Department of Cardiology and Angiology, Hannover Medical School; 30625 Hannover, Germany
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7
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Baron DM, Fenton AR, Saez-Atienzar S, Giampetruzzi A, Sreeram A, Shankaracharya, Keagle PJ, Doocy VR, Smith NJ, Danielson EW, Andresano M, McCormack MC, Garcia J, Bercier V, Van Den Bosch L, Brent JR, Fallini C, Traynor BJ, Holzbaur ELF, Landers JE. ALS-associated KIF5A mutations abolish autoinhibition resulting in a toxic gain of function. Cell Rep 2022; 39:110598. [PMID: 35385738 PMCID: PMC9134378 DOI: 10.1016/j.celrep.2022.110598] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/02/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Understanding the pathogenic mechanisms of disease mutations is critical to advancing treatments. ALS-associated mutations in the gene encoding the microtubule motor KIF5A result in skipping of exon 27 (KIF5AΔExon27) and the encoding of a protein with a novel 39 amino acid residue C-terminal sequence. Here, we report that expression of ALS-linked mutant KIF5A results in dysregulated motor activity, cellular mislocalization, altered axonal transport, and decreased neuronal survival. Single-molecule analysis revealed that the altered C terminus of mutant KIF5A results in a constitutively active state. Furthermore, mutant KIF5A possesses altered protein and RNA interactions and its expression results in altered gene expression/splicing. Taken together, our data support the hypothesis that causative ALS mutations result in a toxic gain of function in the intracellular motor KIF5A that disrupts intracellular trafficking and neuronal homeostasis.
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Affiliation(s)
- Desiree M Baron
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Adam R Fenton
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sara Saez-Atienzar
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Anthony Giampetruzzi
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Aparna Sreeram
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shankaracharya
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Pamela J Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Victoria R Doocy
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan J Smith
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Eric W Danielson
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Megan Andresano
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mary C McCormack
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jaqueline Garcia
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Valérie Bercier
- KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Ludo Van Den Bosch
- KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Jonathan R Brent
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA; George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA; Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA; Therapeutic Development Branch, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Erika L F Holzbaur
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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8
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Lee GKC, Kang H, Beeler-Marfisi J, Sears W, Lillie BN, Bienzle D. Effects of equine SALSA on neutrophil phagocytosis and macrophage cytokine production. PLoS One 2022; 17:e0264911. [PMID: 35286327 PMCID: PMC8920288 DOI: 10.1371/journal.pone.0264911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
Salivary scavenger and agglutinin (SALSA) is a secreted protein with various immunomodulatory roles. In humans, the protein agglutinates and inactivates microorganisms, and inhibits the release of pro-inflammatory cytokines. Saliva, which is rich in SALSA, accelerates bacterial phagocytosis, but SALSA’s contribution is unclear. In horses, the functions of SALSA in inflammation remain undetermined, so they were investigated through phagocytosis and cytokine assays. Equine SALSA was purified from duodenal tissue, which contains abundant SALSA. To assess phagocytosis, fluorescently-labelled bacteria were incubated with 20, 10, 5, or 2.5 μg/mL of SALSA or phosphate buffered saline (PBS), and then incubated at 37°C or on ice with whole blood from seven healthy horses. Fluorescence was measured by gating on neutrophils using a flow cytometer, and compared between groups. To assess effects on cytokine production, alveolar macrophages were isolated from bronchoalveolar lavage fluid of five healthy horses and cultured in serum-free media for 24 hours with different concentrations of SALSA plus 1 μg/mL lipopolysaccharide (LPS), only LPS, or only media. Cytokines were measured in supernatant using an equine-specific multiplex bead immunoassay. There was significantly greater phagocytosis in samples incubated at 37°C compared to incubation on ice. Samples incubated with 20 μg/mL of SALSA at 37°C had less phagocytosis compared to samples with 10 or 2.5 μg/mL SALSA, or PBS. Alveolar macrophages incubated with SALSA plus LPS released significantly less CXC motif chemokine ligand 1, interleukin-8, interleukin-10, and tumor necrosis factor α, and more granulocyte colony stimulating factor (G-CSF), compared to macrophages incubated with LPS alone. These findings indicate anti-inflammatory effects, which may be due to interference with toll-like receptor 4 recognition of LPS or downstream signaling. Increase in G-CSF following incubation with SALSA suggests a novel mechanism for immunoregulation of alveolar macrophages by SALSA, addressing a knowledge gap regarding its functions in horses.
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Affiliation(s)
- Gary Kwok Cheong Lee
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Heng Kang
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | | | - William Sears
- Department of Population Medicine, University of Guelph, Guelph, Ontario, Canada
| | - Brandon N. Lillie
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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9
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Munteanu CVA, Chirițoiu GN, Chirițoiu M, Ghenea S, Petrescu AJ, Petrescu ȘM. Affinity proteomics and deglycoproteomics uncover novel EDEM2 endogenous substrates and an integrative ERAD network. Mol Cell Proteomics 2021; 20:100125. [PMID: 34332121 PMCID: PMC8455867 DOI: 10.1016/j.mcpro.2021.100125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 07/09/2021] [Accepted: 07/25/2021] [Indexed: 02/08/2023] Open
Abstract
Various pathologies result from disruptions to or stress of endoplasmic reticulum (ER) homeostasis, such as Parkinson's disease and most neurodegenerative illnesses, diabetes, pulmonary fibrosis, viral infections and cancers. A critical process in maintaining ER homeostasis is the selection of misfolded proteins by the ER quality-control system (ERQC) for destruction via ER-associated degradation (ERAD). One key protein proposed to act during the first steps of misfolded glycoprotein degradation is the ER degradation-enhancing α-mannosidase-like protein 2 (EDEM2). Therefore, characterization of the EDEM2 associated proteome is of great interest. We took advantage of using melanoma cells overexpressing EDEM2 as a cancer model system, to start documenting at the deglycoproteome level (N-glycosites identification) the emerging link between ER homeostasis and cancer progression. The dataset created for identifying the EDEM2 glyco-clients carrying high mannose/hybrid N-glycans provides a comprehensive N-glycosites analysis mapping over 1000 N-glycosites on more than 600 melanoma glycoproteins. To identify EDEM2-associated proteins we used affinity-proteomics and proteome-wide analysis of sucrose density fractionation in an integrative workflow. Using intensity and spectral count-based quantification, we identify seven new EDEM2 partners, all of which are involved in ERQC and ERAD. Moreover, we defined novel endogenous candidates for EDEM2-dependent ERAD by combining deglycoproteomics, SILAC-based proteomics, and biochemical methods. These included tumor antigens and several ER-transiting endogenous melanoma proteins, including ITGA1 and PCDH2, the expression of which was negatively correlated with that of EDEM2. Tumor antigens are key in the antigen presentation process, whilst ITGA1 and PCDH2 are involved in melanoma metastasis and invasion. EDEM2 could therefore have a regulatory role in melanoma through the modulation of these glycoproteins degradation and trafficking. The data presented herein suggest that EDEM2 is involved in ER homeostasis to a greater extent than previously suggested.
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Affiliation(s)
- Cristian V A Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Gabriela N Chirițoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Marioara Chirițoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Simona Ghenea
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Ștefana M Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania.
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10
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Wang JL, Chen WG, Zhang JJ, Xu CJ. Nogo-A-Δ20/EphA4 interaction antagonizes apoptosis of neural stem cells by integrating p38 and JNK MAPK signaling. J Mol Histol 2021; 52:521-537. [PMID: 33555537 DOI: 10.1007/s10735-021-09960-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Nogo-A protein consists of two main extracellular domains: Nogo-66 (rat amino acid [aa] 1019-1083) and Nogo-A-Δ20 (extracellular, active 180 amino acid Nogo-A region), which serve as strong inhibitors of axon regeneration in the adult CNS (Central Nervous System). Although receptors S1PR2 and HSPGs have been identified as Nogo-A-Δ20 binding proteins, it remains at present elusive whether other receptors directly interacting with Nogo-A-Δ20 exist, and decrease cell death. On the other hand, the key roles of EphA4 in the regulation of glioblastoma, axon regeneration and NSCs (Neural Stem Cells) proliferation or differentiation are well understood, but little is known the relationship between EphA4 and Nogo-A-Δ20 in NSCs apoptosis. Thus, we aim to determine whether Nogo-A-Δ20 can bind to EphA4 and affect survival of NSCs. Here, we discover that EphA4, belonging to a member of erythropoietin-producing hepatocellular (Eph) receptors family, could be acting as a high affinity ligand for Nogo-A-Δ20. Trans-membrane protein of EphA4 is needed for Nogo-A-Δ20-triggered inhibition of NSCs apoptosis, which are mediated by balancing p38 inactivation and JNK MAPK pathway activation. Finally, we predict at the atomic level that essential residues Lys-205, Ile-190, Pro-194 in Nogo-A-Δ20 and EphA4 residues Gln-390, Asn-425, Pro-426 might play critical roles in Nogo-A-Δ20/EphA4 binding via molecular docking.
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Affiliation(s)
- Jun-Ling Wang
- Center for Reproductive Medicine, Affiliated Hospital 1 of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Wei-Guang Chen
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jia-Jia Zhang
- School of 1St Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Chao-Jin Xu
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China.
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11
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Perner J, Helm D, Haberkant P, Hatalova T, Kropackova S, Ribeiro JM, Kopacek P. The Central Role of Salivary Metalloproteases in Host Acquired Resistance to Tick Feeding. Front Cell Infect Microbiol 2020; 10:563349. [PMID: 33312963 PMCID: PMC7708348 DOI: 10.3389/fcimb.2020.563349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/20/2020] [Indexed: 01/07/2023] Open
Abstract
During feeding on vertebrate hosts, ticks secrete saliva composed of a rich cocktail of bioactive molecules modulating host immune responses. Although most of the proteinaceous fraction of tick saliva is of little immunogenicity, repeated feeding of ticks on mammalian hosts may lead to impairment of tick feeding, preventing full engorgement. Here, we challenged rabbits with repeated feeding of both Ixodes ricinus nymphs and adults and observed the formation of specific antibodies against several tick salivary proteins. Repeated feeding of both I. ricinus stages led to a gradual decrease in engorged weights. To identify the salivary antigens, isolated immunoglobulins from repeatedly infested rabbits were utilized for a protein pull-down from the saliva of pilocarpine-treated ticks. Eluted antigens were first identified by peptide mass fingerprinting with the aid of available I. ricinus salivary gland transcriptomes originating from early phases of tick feeding. To increase the authenticity of immunogens identified, we also performed, for the first time, de novo assembly of the sialome from I. ricinus females fed for six days, a timepoint used for pilocarpine-salivation. The most dominant I. ricinus salivary immunogens identified in our study were zinc-dependent metalloproteases of three different families. To corroborate the role of metalloproteases at the tick/host interface, we fed ticks micro-injected with a zinc metalloprotease inhibitor, phosphoramidon, on a rabbit. These ticks clearly failed to initiate feeding and to engorge. However, neither feeding to ticks immune blood of repeatedly infested rabbits, nor phosphoramidon injection into ticks, prevented their engorgement when fed in vitro on an artificial membrane system. These data show that Zn metalloproteases play a decisive role in the success of tick feeding, mediated by complex molecular interactions between the host immune, inflammatory, and hemostatic processes, which are absent in in vitro feeding. This basic concept warrants further investigation and reconsideration of the current strategies towards the development of an effective “anti-tick” vaccine.
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Affiliation(s)
- Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Dominic Helm
- Proteomics Core Facility, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tereza Hatalova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Sara Kropackova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | - Jose M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Petr Kopacek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
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12
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Smalley JL, Kontou G, Choi C, Ren Q, Albrecht D, Abiraman K, Santos MAR, Bope CE, Deeb TZ, Davies PA, Brandon NJ, Moss SJ. Isolation and Characterization of Multi-Protein Complexes Enriched in the K-Cl Co-transporter 2 From Brain Plasma Membranes. Front Mol Neurosci 2020; 13:563091. [PMID: 33192291 PMCID: PMC7643010 DOI: 10.3389/fnmol.2020.563091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Kcc2 plays a critical role in determining the efficacy of synaptic inhibition, however, the cellular mechanisms neurons use to regulate its membrane trafficking, stability and activity are ill-defined. To address these issues, we used affinity purification to isolate stable multi-protein complexes of K-Cl Co-transporter 2 (Kcc2) from the plasma membrane of murine forebrain. We resolved these using blue-native polyacrylamide gel electrophoresis (BN-PAGE) coupled to LC-MS/MS and label-free quantification. Data are available via ProteomeXchange with identifier PXD021368. Purified Kcc2 migrated as distinct molecular species of 300, 600, and 800 kDa following BN-PAGE. In excess of 90% coverage of the soluble N- and C-termini of Kcc2 was obtained. In total we identified 246 proteins significantly associated with Kcc2. The 300 kDa species largely contained Kcc2, which is consistent with a dimeric quaternary structure for this transporter. The 600 and 800 kDa species represented stable multi-protein complexes of Kcc2. We identified a set of novel structural, ion transporting, immune related and signaling protein interactors, that are present at both excitatory and inhibitory synapses, consistent with the proposed localization of Kcc2. These included spectrins, C1qa/b/c and the IP3 receptor. We also identified interactors more directly associated with phosphorylation; Akap5, Akap13, and Lmtk3. Finally, we used LC-MS/MS on the same purified endogenous plasma membrane Kcc2 to detect phosphorylation sites. We detected 11 sites with high confidence, including known and novel sites. Collectively our experiments demonstrate that Kcc2 is associated with components of the neuronal cytoskeleton and signaling molecules that may act to regulate transporter membrane trafficking, stability, and activity.
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Affiliation(s)
- Joshua L Smalley
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Georgina Kontou
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States.,AstraZeneca Tufts Lab for Basic and Translational Neuroscience, Boston, MA, United States
| | - Catherine Choi
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Qiu Ren
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - David Albrecht
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States.,AstraZeneca Tufts Lab for Basic and Translational Neuroscience, Boston, MA, United States
| | - Krithika Abiraman
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States.,AstraZeneca Tufts Lab for Basic and Translational Neuroscience, Boston, MA, United States
| | | | - Christopher E Bope
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Tarek Z Deeb
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States.,AstraZeneca Tufts Lab for Basic and Translational Neuroscience, Boston, MA, United States
| | - Paul A Davies
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Nicholas J Brandon
- AstraZeneca Tufts Lab for Basic and Translational Neuroscience, Boston, MA, United States.,Neuroscience, IMED Biotech Unit, AstraZeneca, Boston, MA, United States
| | - Stephen J Moss
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States.,Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom
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13
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TMBIM6/BI-1 contributes to cancer progression through assembly with mTORC2 and AKT activation. Nat Commun 2020; 11:4012. [PMID: 32782388 PMCID: PMC7419509 DOI: 10.1038/s41467-020-17802-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 07/16/2020] [Indexed: 01/09/2023] Open
Abstract
Transmembrane B cell lymphoma 2-associated X protein inhibitor motif-containing (TMBIM) 6, a Ca2+ channel-like protein, is highly up-regulated in several cancer types. Here, we show that TMBIM6 is closely associated with survival in patients with cervical, breast, lung, and prostate cancer. TMBIM6 deletion or knockdown suppresses primary tumor growth. Further, mTORC2 activation is up-regulated by TMBIM6 and stimulates glycolysis, protein synthesis, and the expression of lipid synthesis genes and glycosylated proteins. Moreover, ER-leaky Ca2+ from TMBIM6, a unique characteristic, is shown to affect mTORC2 assembly and its association with ribosomes. In addition, we identify that the BIA compound, a potentialTMBIM6 antagonist, prevents TMBIM6 binding to mTORC2, decreases mTORC2 activity, and also regulates TMBIM6-leaky Ca2+, further suppressing tumor formation and progression in cancer xenograft models. This previously unknown signaling cascade in which mTORC2 activity is enhanced via the interaction with TMBIM6 provides potential therapeutic targets for various malignancies. TMBIM6, a member of the transmembrane BI-1 motif-containing family of proteins, is overexpressed in many cancer types. Here, the authors show that TMBIM6 regulates AKT activation through mTORC2 assembly and ribosome association and identify an antagonist of TMBIM6 with anti-tumor properties.
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14
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Chiritoiu M, Chiritoiu GN, Munteanu CVA, Pastrama F, Ivessa NE, Petrescu SM. EDEM1 Drives Misfolded Protein Degradation via ERAD and Exploits ER-Phagy as Back-Up Mechanism When ERAD Is Impaired. Int J Mol Sci 2020; 21:ijms21103468. [PMID: 32423001 PMCID: PMC7279049 DOI: 10.3390/ijms21103468] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 01/20/2023] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is the main mechanism of targeting ER proteins for degradation to maintain homeostasis, and perturbations of ERAD lead to pathological conditions. ER-degradation enhancing α-mannosidase-like (EDEM1) was proposed to extract terminally misfolded proteins from the calnexin folding cycle and target them for degradation by ERAD. Here, using mass-spectrometry and biochemical methods, we show that EDEM1 is found in auto-regulatory complexes with ERAD components. Moreover, the N-terminal disordered region of EDEM1 mediates protein–protein interaction with misfolded proteins, whilst the absence of this domain significantly impairs their degradation. We also determined that overexpression of EDEM1 can induce degradation, even when proteasomal activity is severely impaired, by promoting the formation of aggregates, which can be further degraded by autophagy. Therefore, we propose that EDEM1 maintains ER homeostasis and mediates ERAD client degradation via autophagy when either dislocation or proteasomal degradation are impaired.
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Affiliation(s)
- Marioara Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Gabriela N. Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Cristian V. A. Munteanu
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - Florin Pastrama
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - N. Erwin Ivessa
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, A-1030 Vienna, Austria;
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
- Correspondence: ; Tel.: +40-2-1223-9069
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15
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Zhang Y, Natale R, Domingues AP, Toleco MR, Siemiatkowska B, Fàbregas N, Fernie AR. Rapid Identification of Protein-Protein Interactions in Plants. ACTA ACUST UNITED AC 2020; 4:e20099. [PMID: 31714676 DOI: 10.1002/cppb.20099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzyme-enzyme interactions can be discovered by affinity purification mass spectrometry (AP-MS) under in vivo conditions. Tagged enzymes can either be transiently transformed into plant leaves or stably transformed into plant cells prior to AP-MS. The success of AP-MS depends on the levels and stability of the bait protein, the stability of the protein-protein interactions, and the efficiency of trypsin digestion and recovery of tryptic peptides for MS analysis. Unlike in-gel-digestion AP-MS, in which the gel is cut into pieces for several independent trypsin digestions, we uses a proteomics-based in-solution digestion method to directly digest the proteins on the beads following affinity purification. Thus, a single replicate within an AP-MS experiment constitutes a single sample for LC-MS measurement. In subsequent data analysis, normalized signal intensities can be processed to determine fold-change abundance (FC-A) scores by use of the SAINT algorithm embedded within the CRAPome software. Following analysis of co-sublocalization of "bait" and "prey," we suggest considering only the protein pairs for which the intensities were more than 2% compared with the bait, corresponding to FC-A values of at least four within-biological replicates, which we recommend as minimum. If the procedure is faithfully followed, experimental assessment of enzyme-enzyme interactions can be carried out in Arabidopsis within 3 weeks (transient expression) or 5 weeks (stable expression). © 2019 The Authors. Basic Protocol 1: Gene cloning to the destination vectors Alternate Protocol: In-Fusion or Gibson gene cloning protocol Basic Protocol 2: Transformation of baits into the plant cell culture or plant leaf Basic Protocol 3: Affinity purification of protein complexes Basic Protocol 4: On-bead trypsin/LysC digestion and C18 column peptide desalting and concentration Basic Protocol 5: Data analysis and quality control.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Roberto Natale
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.,Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Adilson Pereira Domingues
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany.,Department of Crop Science, Luiz de Queiroz College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Mitchell Rey Toleco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Beata Siemiatkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Norma Fàbregas
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
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16
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Dam DHM, Jelsma SA, Yu JM, Liu H, Kong B, Paller AS. Flotillin and AP2A1/2 Promote IGF-1 Receptor Association with Clathrin and Internalization in Primary Human Keratinocytes. J Invest Dermatol 2020; 140:1743-1752.e4. [PMID: 32027876 DOI: 10.1016/j.jid.2020.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/21/2022]
Abstract
IGF-1 receptor (IGF1R) signaling promotes keratinocyte proliferation, migration, and survival. However, the mechanism of IGF1R endocytosis in normal keratinocytes remains unclear. Confocal, super resolution structured illumination microscopy, total internal reflection fluorescence microscopy, and coimmunoprecipitation studies reveal that IGF1R associates with flotillin-1 (Flot-1), which currently has no known role in normal receptor tyrosine kinase endocytosis, under basal conditions in monolayer keratinocyte cultures. Ligand stimulation of IGF1R promotes its clathrin-dependent endocytosis, mediated by two distinct adaptors, Flot-1 in noncaveolar lipid rafts and the AP2A1/2 complex in clathrin vesicles. Concurrent, but not individual, short hairpin RNA knockdown of FLOT1/2 and AP2A1/2 reduced IGF1R association with clathrin, internalization, and pathway activation by more than 50% (of phosphorylated IGF1R, phosphorylated protein kinase B, and phosphorylated MAPK kinase), suggesting the complementarity of these two adaptor-specific pathways. The Flot-1 pathway is more responsive to low IGF-1 concentrations, whereas the AP2A1/2 pathway predominates at higher IGF-1 concentrations. Selective association of IGF1R-Flot-1-clathrin with Rab4, but IGF1R-AP2A1/2-clathrin with Rab11, implicates Flot-1 as the adaptor for faster recycling and AP2A1/2 as the adaptor for slower IGF1R recycling. These dual pathways, particularly flotillin-dependent, clathrin-mediated endocytosis, provide a new avenue for drug targeting in disorders with aberrant regulation of IGF1R signaling.
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Affiliation(s)
- Duncan Hieu M Dam
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sophia A Jelsma
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jeong Min Yu
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Haoming Liu
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Betty Kong
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amy S Paller
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
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17
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Thatikonda S, Pooladanda V, Sigalapalli DK, Godugu C. Piperlongumine regulates epigenetic modulation and alleviates psoriasis-like skin inflammation via inhibition of hyperproliferation and inflammation. Cell Death Dis 2020; 11:21. [PMID: 31924750 PMCID: PMC6954241 DOI: 10.1038/s41419-019-2212-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 12/27/2022]
Abstract
Psoriasis is an autoimmune skin disease, where chronic immune responses due to exaggerated cytokine signaling, abnormal differentiation, and evasion of keratinocytes apoptosis plays a crucial role in mediating abnormal keratinocytes hyperproliferation. From the therapeutic perspective, the molecules with strong anti-proliferative and anti-inflammatory properties could have tremendous relevance. In this study, we demonstrated that piperlongumine (PPL) treatment effectively abrogated the hyperproliferation and differentiation of keratinocytes by inducing ROS-mediated late apoptosis with loss of mitochondrial membrane potential. Besides, the arrest of cell cycle was found at Sub-G1 phase as a result of DNA fragmentation. Molecularly, inhibition of STAT3 and Akt signaling was observed with a decrease in proliferative markers such as PCNA, ki67, and Cyclin D1 along with anti-apoptotic Bcl-2 protein expression. Keratin 17 is a critical regulator of keratinocyte differentiation, and it was found to be downregulated with PPL significantly. Furthermore, prominent anti-inflammatory effects were observed by inhibition of lipopolysaccharide (LPS)/Imiquimod (IMQ)-induced p65 NF-κB signaling cascade and strongly inhibited the production of cytokine storm involved in psoriasis-like skin inflammation, thus led to the restoration of normal epidermal architecture with reduction of epidermal hyperplasia and splenomegaly. In addition, PPL epigenetically inhibited histone-modifying enzymes, which include histone deacetylases (HDACs) of class I (HDAC1-4) and class II (HDAC6) evaluated by immunoblotting and HDAC enzyme assay kit. In addition, our results show that PPL effectively inhibits the nuclear translocation of p65 and a histone modulator HDAC3, thus sequestered in the cytoplasm of macrophages. Furthermore, PPL effectively enhanced the protein-protein interactions of HDAC3 and p65 with IκBα, which was disrupted by LPS stimulation and were evaluated by Co-IP and molecular modeling. Collectively, our findings indicate that piperlongumine may serve as an anti-proliferative and anti-inflammatory agent and could serve as a potential therapeutic option in treating psoriasis.
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Affiliation(s)
- Sowjanya Thatikonda
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Venkatesh Pooladanda
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Dilep Kumar Sigalapalli
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Chandraiah Godugu
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India.
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18
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Welch CJ, Talaga ML, Kadav PD, Edwards JL, Bandyopadhyay P, Dam TK. A capture and release method based on noncovalent ligand cross-linking and facile filtration for purification of lectins and glycoproteins. J Biol Chem 2020; 295:223-236. [PMID: 31792056 PMCID: PMC6952606 DOI: 10.1074/jbc.ra119.010625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/22/2019] [Indexed: 12/26/2022] Open
Abstract
Glycan-binding proteins such as lectins are ubiquitous proteins that mediate many biological functions. To study their various biological activities and structure-function relationships, researchers must use lectins in their purest form. Conventional purification techniques, especially affinity column chromatography, have been instrumental in isolating numerous lectins and glycoproteins. These approaches, however, are time-consuming, consist of multiple steps, and often require extensive trial-and-error experimentation. Therefore, techniques that are relatively rapid and facile are needed. Here we describe such a technique, called capture and release (CaRe). The strength of this approach is rooted in its simplicity and accuracy. CaRe purifies lectins by utilizing their ability to form spontaneous noncovalently cross-linked complexes with specific multivalent ligands. The lectins are captured in the solution phase by multivalent capturing agents, released by competitive monovalent ligands, and then separated by filtration. CaRe does not require antibodies, solid affinity matrices, specialized detectors, a customized apparatus, controlled environments, or functionalization or covalent modification of reagents. CaRe is a time-saving procedure that can purify lectins even from a few milliliters of crude protein extracts. We validated CaRe by purifying recombinant human galectin-3 and five other known lectins and also tested CaRe's ability to purify glycoproteins. Besides purifying lectins and glycoproteins, CaRe has the potential to purify other glycoconjugates, including proteoglycans. This technique could also be used for nonlectin proteins that bind multivalent ligands. Given the ubiquity of glycosylation in nature, we anticipate that CaRe has broad utility.
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Affiliation(s)
- Christina J Welch
- Laboratory of Mechanistic Glycobiology, Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Melanie L Talaga
- Laboratory of Mechanistic Glycobiology, Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Priyanka D Kadav
- Laboratory of Mechanistic Glycobiology, Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Jared L Edwards
- Laboratory of Mechanistic Glycobiology, Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Purnima Bandyopadhyay
- Laboratory of Mechanistic Glycobiology, Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Tarun K Dam
- Laboratory of Mechanistic Glycobiology, Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931; Health Research Institute, Michigan Technological University, Houghton, Michigan 49931.
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19
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Adenylyl Cyclase Type 8 Overexpression Impairs Phosphorylation-Dependent Orai1 Inactivation and Promotes Migration in MDA-MB-231 Breast Cancer Cells. Cancers (Basel) 2019; 11:cancers11111624. [PMID: 31652779 PMCID: PMC6893434 DOI: 10.3390/cancers11111624] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/26/2022] Open
Abstract
Orai1 plays a major role in store-operated Ca2+ entry (SOCE) in triple-negative breast cancer (TNBC) cells. This channel is inactivated via different mechanisms, including protein kinase C (PKC) and protein kinase A (PKA)-dependent phosphorylation at Ser-27 and Ser-30 or Ser-34, respectively, which shapes the Ca2+ responses to agonists. The Ca2+ calmodulin-activated adenylyl cyclase type 8 (AC8) was reported to interact directly with Orai1, thus mediating a dynamic interplay between the Ca2+- and cyclic adenosine monophosphate (cAMP)-dependent signaling pathways. Here, we show that the breast cancer cell lines MCF7 and MDA-MB-231 exhibit enhanced expression of Orai1 and AC8 as compared to the non-tumoral breast epithelial MCF10A cell line. In these cells, AC8 interacts with the Orai1α variant in a manner that is not regulated by Orai1 phosphorylation. AC8 knockdown in MDA-MB-231 cells, using two different small interfering RNAs (siRNAs), attenuates thapsigargin (TG)-induced Ca2+ entry and also Ca2+ influx mediated by co-expression of Orai1 and the Orai1-activating small fragment (OASF) of STIM1 (stromal interaction molecule-1). Conversely, AC8 overexpression enhances SOCE, as well as Ca2+ entry, in cells co-expressing Orai1 and OASF. In MDA-MB-231 cells, we found that AC8 overexpression reduces the Orai1 phosphoserine content, thus suggesting that AC8 interferes with Orai1 serine phosphorylation, which takes place at residues located in the AC8-binding site. Consistent with this, the subset of Orai1 associated with AC8 in naïve MDA-MB-231 cells is not phosphorylated in serine residues in contrast to the AC8-independent Orai1 subset. AC8 expression knockdown attenuates migration of MCF7 and MDA-MB-231 cells, while this maneuver has no effect in the MCF10A cell line, which is likely attributed to the low expression of AC8 in these cells. We found that AC8 is required for FAK (focal adhesion kinase) phosphorylation in MDA-MB-231 cells, which might explain its role in cell migration. Finally, we found that AC8 is required for TNBC cell proliferation. These findings indicate that overexpression of AC8 in breast cancer MDA-MB-231 cells impairs the phosphorylation-dependent Orai1 inactivation, a mechanism that might support the enhanced ability of these cells to migrate.
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20
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Investigating the role of Ebp1 in Chandipura virus infection. J Biosci 2019. [DOI: 10.1007/s12038-019-9847-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Dey D, Honda A, Chattopadhyay D. Investigating the role of Ebp1 in Chandipura virus infection. J Biosci 2019; 44:31. [PMID: 31180044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
ErbB-3 binding protein 1 (Ebp1) is a host protein which binds ErbB-3 receptor to induce signalling events for cell growth regulation. In addition, Ebp1 also interacts with ribonucleoprotein complexes. In recent times, Ebp1 was found to play an antagonistic role in viral infections caused by Influenza and Rinderpest viruses. In our present work we have tried to understand the role of Ebp1 in Chandipura virus (CHPV) infection. We have observed an induction in Ebp1 expression upon CHPV infection similar to other viruses. However, unlike other viruses an overexpressed Ebp1 only reduces viral protein expression, but does not affect its progeny formation. Additionally, this effect is being carried out in an indirect manner, as there is no interaction between Ebp1 and viral proteins. This is despite Ebp1's presence in viral inclusion bodies.
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Affiliation(s)
- Dhritiman Dey
- Department of Biotechnology, University of Calcutta, Calcutta, India
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22
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Profiling Optimal Conditions for Capturing EDEM Proteins Complexes in Melanoma Using Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:155-167. [PMID: 31347047 DOI: 10.1007/978-3-030-15950-4_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Endoplasmic reticulum (ER) resident and secretory proteins that fail to reach their native conformation are selected for degradation through the ER-Associated Degradation (ERAD) pathway. The ER degradation-enhancing alpha-mannosidase-like proteins (EDEMs) were shown to be involved in this pathway but their precise role is still under investigation. Mass spectrometry analysis has contributed significantly to the characterization of protein complexes in the last years. The recent advancements in instrumentation, especially within resolution and speed can provide unique insights concerning the molecular architecture of protein-protein interactions in systems biology. Previous reports have suggested that several protein complexes in ERAD are sensitive to the extraction conditions. Indeed, whilst EDEM proteins can be recovered in most detergents, some of their partners are not solubilized, which further emphasizes the importance of the experimental setup. Here, we define such dynamic interactions of EDEM proteins by employing offline protein fractionation, nanoLC-MS/MS and describe how mass spectrometry can contribute to the characterization of such complexes, particularly within a disease context like melanoma.
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23
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Pellacani C, Bucciarelli E, Renda F, Hayward D, Palena A, Chen J, Bonaccorsi S, Wakefield JG, Gatti M, Somma MP. Splicing factors Sf3A2 and Prp31 have direct roles in mitotic chromosome segregation. eLife 2018; 7:40325. [PMID: 30475206 PMCID: PMC6287947 DOI: 10.7554/elife.40325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/14/2018] [Indexed: 12/26/2022] Open
Abstract
Several studies have shown that RNAi-mediated depletion of splicing factors (SFs) results in mitotic abnormalities. However, it is currently unclear whether these abnormalities reflect defective splicing of specific pre-mRNAs or a direct role of the SFs in mitosis. Here, we show that two highly conserved SFs, Sf3A2 and Prp31, are required for chromosome segregation in both Drosophila and human cells. Injections of anti-Sf3A2 and anti-Prp31 antibodies into Drosophila embryos disrupt mitotic division within 1 min, arguing strongly against a splicing-related mitotic function of these factors. We demonstrate that both SFs bind spindle microtubules (MTs) and the Ndc80 complex, which in Sf3A2- and Prp31-depleted cells is not tightly associated with the kinetochores; in HeLa cells the Ndc80/HEC1-SF interaction is restricted to the M phase. These results indicate that Sf3A2 and Prp31 directly regulate interactions among kinetochores, spindle microtubules and the Ndc80 complex in both Drosophila and human cells.
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Affiliation(s)
- Claudia Pellacani
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Elisabetta Bucciarelli
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Fioranna Renda
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Daniel Hayward
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Antonella Palena
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Jack Chen
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Silvia Bonaccorsi
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - James G Wakefield
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Maurizio Gatti
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy.,Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Maria Patrizia Somma
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
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24
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Ying G, Boldt K, Ueffing M, Gerstner CD, Frederick JM, Baehr W. The small GTPase RAB28 is required for phagocytosis of cone outer segments by the murine retinal pigmented epithelium. J Biol Chem 2018; 293:17546-17558. [PMID: 30228185 PMCID: PMC6231133 DOI: 10.1074/jbc.ra118.005484] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/12/2018] [Indexed: 12/19/2022] Open
Abstract
RAB28, a member of the RAS oncogene family, is a ubiquitous, farnesylated, small GTPase of unknown function present in photoreceptors and the retinal pigmented epithelium (RPE). Nonsense mutations of the human RAB28 gene cause recessive cone-rod dystrophy 18 (CRD18), characterized by macular hyperpigmentation, progressive loss of visual acuity, RPE atrophy, and severely attenuated cone and rod electroretinography (ERG) responses. In an attempt to elucidate the disease-causing mechanism, we generated Rab28-/- mice by deleting exon 3 and truncating RAB28 after exon 2. We found that Rab28-/- mice recapitulate features of the human dystrophy (i.e. they exhibited reduced cone and rod ERG responses and progressive retina degeneration). Cones of Rab28-/- mice extended their outer segments (OSs) to the RPE apical processes and formed enlarged, balloon-like distal tips before undergoing degeneration. The visual pigment content of WT and Rab28-/- cones was comparable before the onset of degeneration. Cone phagosomes were almost absent in Rab28-/- mice, whereas rod phagosomes displayed normal levels. A protein-protein interaction screen identified several RAB28-interacting proteins, including the prenyl-binding protein phosphodiesterase 6 δ-subunit (PDE6D) and voltage-gated potassium channel subfamily J member 13 (KCNJ13) present in the RPE apical processes. Of note, the loss of PDE6D prevented delivery of RAB28 to OSs. Taken together, these findings reveal that RAB28 is required for shedding and phagocytosis of cone OS discs.
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Affiliation(s)
- Guoxin Ying
- From the Department of Ophthalmology and Visual Sciences, University of Utah Health Science Center, Salt Lake City, Utah 84132,
| | - Karsten Boldt
- the Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany, and
| | - Marius Ueffing
- the Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany, and
| | - Cecilia D Gerstner
- From the Department of Ophthalmology and Visual Sciences, University of Utah Health Science Center, Salt Lake City, Utah 84132
| | - Jeanne M Frederick
- From the Department of Ophthalmology and Visual Sciences, University of Utah Health Science Center, Salt Lake City, Utah 84132
| | - Wolfgang Baehr
- From the Department of Ophthalmology and Visual Sciences, University of Utah Health Science Center, Salt Lake City, Utah 84132,
- the Departments of Neurobiology and Anatomy and
- Biology, University of Utah, Salt Lake City, Utah 84112
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25
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Davies AK, Itzhak DN, Edgar JR, Archuleta TL, Hirst J, Jackson LP, Robinson MS, Borner GHH. AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A. Nat Commun 2018; 9:3958. [PMID: 30262884 PMCID: PMC6160451 DOI: 10.1038/s41467-018-06172-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/17/2018] [Indexed: 12/03/2022] Open
Abstract
Adaptor protein 4 (AP-4) is an ancient membrane trafficking complex, whose function has largely remained elusive. In humans, AP-4 deficiency causes a severe neurological disorder of unknown aetiology. We apply unbiased proteomic methods, including 'Dynamic Organellar Maps', to find proteins whose subcellular localisation depends on AP-4. We identify three transmembrane cargo proteins, ATG9A, SERINC1 and SERINC3, and two AP-4 accessory proteins, RUSC1 and RUSC2. We demonstrate that AP-4 deficiency causes missorting of ATG9A in diverse cell types, including patient-derived cells, as well as dysregulation of autophagy. RUSC2 facilitates the transport of AP-4-derived, ATG9A-positive vesicles from the trans-Golgi network to the cell periphery. These vesicles cluster in close association with autophagosomes, suggesting they are the "ATG9A reservoir" required for autophagosome biogenesis. Our study uncovers ATG9A trafficking as a ubiquitous function of the AP-4 pathway. Furthermore, it provides a potential molecular pathomechanism of AP-4 deficiency, through dysregulated spatial control of autophagy.
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Affiliation(s)
- Alexandra K Davies
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Tara L Archuleta
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.
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26
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Navarro Negredo P, Edgar JR, Manna PT, Antrobus R, Robinson MS. The WDR11 complex facilitates the tethering of AP-1-derived vesicles. Nat Commun 2018; 9:596. [PMID: 29426865 PMCID: PMC5807400 DOI: 10.1038/s41467-018-02919-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/02/2018] [Indexed: 12/14/2022] Open
Abstract
Vesicluar transport of proteins from endosomes to the trans-Golgi network (TGN) is an essential cellular pathway, but much of its machinery is still unknown. A screen for genes involved in endosome-to-TGN trafficking produced two hits, the adaptor protein-1 (AP-1 complex), which facilitates vesicle budding, and WDR11. Here we demonstrate that WDR11 forms a stable complex with two other proteins, which localises to the TGN region and does not appear to be associated with AP-1, suggesting it may act downstream from budding. In a vesicle tethering assay, capture of vesicles by golgin-245 was substantially reduced in WDR11-knockout cells. Moreover, structured illumination microscopy and relocation assays indicate that the WDR11 complex is initially recruited onto vesicles rather than the TGN, where it may in turn recruit the golgin binding partner TBC1D23. We propose that the complex acts together with TBC1D23 to facilitate the golgin-mediated capture of vesicles that were generated using AP-1. Trafficking from endosomes to the trans-Golgi network requires recognition of vesicle tethers during membrane docking. Here, the authors identify a complex localised to AP-1 generated vesicles containing WDR11, C17orf75 and FAM91A, which together with TBC1D23 facilitates vesicle capture on Golgi membranes
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Affiliation(s)
- Paloma Navarro Negredo
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Paul T Manna
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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27
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Ullah K, Rosendahl AH, Izzi V, Bergmann U, Pihlajaniemi T, Mäki JM, Myllyharju J. Hypoxia-inducible factor prolyl-4-hydroxylase-1 is a convergent point in the reciprocal negative regulation of NF-κB and p53 signaling pathways. Sci Rep 2017; 7:17220. [PMID: 29222481 PMCID: PMC5722952 DOI: 10.1038/s41598-017-17376-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/24/2017] [Indexed: 12/14/2022] Open
Abstract
Hypoxia-inducible factor 1α (HIF1α) induces the expression of several hundred genes in hypoxia aiming at restoration of oxygen homeostasis. HIF prolyl-4-hydroxylases (HIF-P4Hs) regulate the stability of HIF1α in an oxygen-dependent manner. Hypoxia is a common feature in inflammation and cancer and the HIF pathway is closely linked with the inflammatory NF-κB and tumor suppressor p53 pathways. Here we show that genetic inactivation or chemical inhibition of HIF-P4H-1 leads to downregulation of proinflammatory genes, while proapoptotic genes are upregulated. HIF-P4H-1 inactivation reduces the inflammatory response under LPS stimulus in vitro and in an acute skin inflammation model in vivo. Furthermore, HIF-P4H-1 inactivation increases p53 activity and stability and hydroxylation of proline 142 in p53 has an important role in this regulation. Altogether, our data suggest that HIF-P4H-1 inhibition may be a promising therapeutic candidate for inflammatory diseases and cancer, enhancing the reciprocal negative regulation of the NF-κB and p53 pathways.
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Affiliation(s)
- Karim Ullah
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, FIN-90014, Finland.,Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, FIN-90014, Finland
| | - Ann-Helen Rosendahl
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, FIN-90014, Finland.,Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, FIN-90014, Finland
| | - Valerio Izzi
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, FIN-90014, Finland.,Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, FIN-90014, Finland
| | - Ulrich Bergmann
- Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland
| | - Taina Pihlajaniemi
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, FIN-90014, Finland.,Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, FIN-90014, Finland
| | - Joni M Mäki
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, FIN-90014, Finland.,Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, FIN-90014, Finland
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, University of Oulu, Oulu, FIN-90014, Finland. .,Biocenter Oulu, University of Oulu, Oulu, FIN-90014, Finland. .,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, FIN-90014, Finland.
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28
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Sódar BW, Kovács Á, Visnovitz T, Pállinger É, Vékey K, Pocsfalvi G, Turiák L, Buzás EI. Best practice of identification and proteomic analysis of extracellular vesicles in human health and disease. Expert Rev Proteomics 2017; 14:1073-1090. [DOI: 10.1080/14789450.2017.1392244] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Barbara W. Sódar
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Árpád Kovács
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Tamás Visnovitz
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Éva Pállinger
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest Hungary
| | - Gabriella Pocsfalvi
- Mass Spectrometry and Proteomics, Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest Hungary
| | - Edit I Buzás
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
- MTA-SE Immunoproteogenomic Extracellular Vesicle Research Group, Hungarian Academy of Sciences, Budapest, Hungary
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29
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Sahu BS, Manna PT, Edgar JR, Antrobus R, Mahata SK, Bartolomucci A, Borner GHH, Robinson MS. Role of clathrin in dense core vesicle biogenesis. Mol Biol Cell 2017; 28:2676-2685. [PMID: 28814506 PMCID: PMC5620375 DOI: 10.1091/mbc.e16-10-0742] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 07/13/2017] [Accepted: 08/07/2017] [Indexed: 11/11/2022] Open
Abstract
The dense core vesicles (DCVs) of neuroendocrine cells are a rich source of bioactive molecules such as peptides, hormones, and neurotransmitters, but relatively little is known about how they are formed. Using fractionation profiling, a method that combines subcellular fractionation with mass spectrometry, we identified ∼1200 proteins in PC12 cell vesicle-enriched fractions, with DCV-associated proteins showing distinct profiles from proteins associated with other types of vesicles. To investigate the role of clathrin in DCV biogenesis, we stably transduced PC12 cells with an inducible short hairpin RNA targeting clathrin heavy chain, resulting in ∼85% protein loss. DCVs could still be observed in the cells by electron microscopy, but mature profiles were approximately fourfold less abundant than in mock-treated cells. By quantitative mass spectrometry, DCV-associated proteins were found to be reduced approximately twofold in clathrin-depleted cells as a whole and approximately fivefold in vesicle-enriched fractions. Our combined data sets enabled us to identify new candidate DCV components. Secretion assays revealed that clathrin depletion causes a near-complete block in secretagogue-induced exocytosis. Taken together, our data indicate that clathrin has a function in DCV biogenesis beyond its established role in removing unwanted proteins from the immature vesicle.
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Affiliation(s)
- Bhavani S Sahu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Paul T Manna
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Sushil K Mahata
- Department of Medicine, Veterans Affairs San Diego Healthcare System, San Diego, CA 92161.,Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Alessandro Bartolomucci
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455
| | - Georg H H Borner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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Abramowicz A, Widlak P, Pietrowska M. Proteomic analysis of exosomal cargo: the challenge of high purity vesicle isolation. MOLECULAR BIOSYSTEMS 2017; 12:1407-19. [PMID: 27030573 DOI: 10.1039/c6mb00082g] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The re-discovery of exosomes as intercellular messengers with high potential for diagnostic and therapeutic utility has led to them becoming a popular topic of research in recent years. One of the essential research areas in this field is the characterization of exosomal cargo, which includes numerous non-randomly packed proteins and nucleic acids. Unexpectedly, a very challenging aspect of exploration of extracellular vesicles has turned out to be their effective and selective isolation. The plurality of developed protocols leads to qualitative and quantitative variability in terms of the obtained exosomes, which significantly affects the results of downstream analyses and makes them difficult to compare, reproduce and interpret between research groups. Currently, there is a general consensus among the exosome-oriented community concerning the urgent need for the optimization and standardization of methods employed for the purification of these vesicles. Hence, we review here several strategies for exosome preparation including ultracentrifugation, chemical precipitation, affinity capturing and filtration techniques. The advantages and disadvantages of different approaches are discussed with special emphasis being placed on their adequacy for proteomics applications, which are particularly sensitive to sample quality. We conclude that certain methods, exemplified by ultracentrifugation combined with iodixanol density gradient centrifugation or gel filtration, although labor-intensive, provide superior quality exosome preparations suitable for reliable analysis by mass spectrometry.
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Affiliation(s)
- Agata Abramowicz
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | - Piotr Widlak
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
| | - Monika Pietrowska
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland.
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Relief of oxidative stress and cardiomyocyte apoptosis by using curcumin nanoparticles. Colloids Surf B Biointerfaces 2017; 153:174-182. [DOI: 10.1016/j.colsurfb.2017.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/15/2017] [Accepted: 02/18/2017] [Indexed: 12/25/2022]
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IL-21 May Promote Granzyme B-Dependent NK/Plasmacytoid Dendritic Cell Functional Interaction in Cutaneous Lupus Erythematosus. J Invest Dermatol 2017; 137:1493-1500. [PMID: 28344062 DOI: 10.1016/j.jid.2017.03.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/14/2017] [Accepted: 03/06/2017] [Indexed: 12/13/2022]
Abstract
Autoimmune skin lesions are characterized by a complex cytokine milieu and by the accumulation of plasmacytoid dendritic cells (pDCs). Granzyme B (GrB) transcript is abundant in activated pDCs, though its mechanisms of regulation and biological role are largely unknown. Here we report that IL-21 was the only T helper 1/T helper 17 cytokine able to induce the expression and secretion of GrB by pDCs and that this action was counteracted by the autocrine production of type I IFNs. In lupus erythematosus skin lesions, the percentage of GrB+ pDCs directly correlated with the IL-21/MxA ratio, indicating that the interplay between these two cytokines finely tunes the levels of pDC-dependent GrB also in vivo. In lupus erythematosus, pDCs colocalized with professional cytotoxic cells at sites of epithelial damage, suggesting a role in keratinocyte killing. Accordingly, we demonstrate that supernatants of IL-21-activated pDCs promoted autologous keratinocyte killing by natural killer cells and this action was dependent on GrB. These results propose a GrB-dependent functional interaction between pDCs and natural killer cells and highlight a negative feedback regulation by type I IFNs in vitro and in vivo that may function to limit excessive tissue damage.
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Myocyte-Derived Hsp90 Modulates Collagen Upregulation via Biphasic Activation of STAT-3 in Fibroblasts during Cardiac Hypertrophy. Mol Cell Biol 2017; 37:MCB.00611-16. [PMID: 28031326 DOI: 10.1128/mcb.00611-16] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 12/16/2016] [Indexed: 01/01/2023] Open
Abstract
Signal transducer and activator of transcription 3 (STAT-3)-mediated signaling in relation to upregulated collagen expression in fibroblasts during cardiac hypertrophy is well defined. Our recent findings have identified heat shock protein 90 (Hsp90) to be a critical modulator of fibrotic signaling in cardiac fibroblasts in this disease milieu. The present study was therefore intended to analyze the role of Hsp90 in the STAT-3-mediated collagen upregulation process. Our data revealed a significant difference between in vivo and in vitro results, pointing to a possible involvement of myocyte-fibroblast cross talk in this process. Cardiomyocyte-targeted knockdown of Hsp90 in rats (Rattus norvegicus) in which the renal artery was ligated showed downregulated collagen synthesis. Furthermore, the results obtained with cardiac fibroblasts conditioned with Hsp90-inhibited hypertrophied myocyte supernatant pointed toward cardiomyocytes' role in the regulation of collagen expression in fibroblasts during hypertrophy. Our study also revealed a novel signaling mechanism where myocyte-derived Hsp90 orchestrates not only p65-mediated interleukin-6 (IL-6) synthesis but also its release in exosomal vesicles. Such myocyte-derived exosomes and myocyte-secreted IL-6 are responsible in unison for the biphasic activation of STAT-3 signaling in cardiac fibroblasts that culminates in excess collagen synthesis, leading to severely compromised cardiac function during cardiac hypertrophy.
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Leney AC, Heck AJR. Native Mass Spectrometry: What is in the Name? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:5-13. [PMID: 27909974 PMCID: PMC5174146 DOI: 10.1007/s13361-016-1545-3] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 05/11/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is nowadays one of the cornerstones of biomolecular mass spectrometry and proteomics. Advances in sample preparation and mass analyzers have enabled researchers to extract much more information from biological samples than just the molecular weight. In particular, relevant for structural biology, noncovalent protein-protein and protein-ligand complexes can now also be analyzed by MS. For these types of analyses, assemblies need to be retained in their native quaternary state in the gas phase. This initial small niche of biomolecular mass spectrometry, nowadays often referred to as "native MS," has come to maturation over the last two decades, with dozens of laboratories using it to study mostly protein assemblies, but also DNA and RNA-protein assemblies, with the goal to define structure-function relationships. In this perspective, we describe the origins of and (re)define the term native MS, portraying in detail what we meant by "native MS," when the term was coined and also describing what it does (according to us) not entail. Additionally, we describe a few examples highlighting what native MS is, showing its successes to date while illustrating the wide scope this technology has in solving complex biological questions. Graphical Abstract ᅟ.
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Affiliation(s)
- Aneika C Leney
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands.
- Netherlands Proteomics Center, Padualaan 8, 3584CH, Utrecht, The Netherlands.
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Geng Q, Xhabija B, Knuckle C, Bonham CA, Vacratsis PO. The Atypical Dual Specificity Phosphatase hYVH1 Associates with Multiple Ribonucleoprotein Particles. J Biol Chem 2016; 292:539-550. [PMID: 27856639 DOI: 10.1074/jbc.m116.715607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/03/2016] [Indexed: 12/30/2022] Open
Abstract
Human YVH1 (hYVH1), also known as dual specificity phosphatase 12 (DUSP12), is a poorly characterized atypical dual specificity phosphatase widely conserved throughout evolution. Recent findings have demonstrated that hYVH1 expression affects cellular DNA content and is a novel cell survival phosphatase preventing both thermal and oxidative stress-induced cell death, whereas studies in yeast have established YVH1 as a novel 60S ribosome biogenesis factor. In this study, we have isolated novel hYVH1-associating proteins from human U2OS osteosarcoma cells using affinity chromatography coupled to mass spectrometry employing ion mobility separation. Numerous ribosomal proteins were identified, confirming the work done in yeast. Furthermore, proteins known to be present on additional RNP particles were identified, including Y box-binding protein 1 (YB-1) and fragile X mental retardation protein, proteins that function in translational repression and stress granule regulation. Follow-up studies demonstrated that hYVH1 co-localizes with YB-1 and fragile X mental retardation protein on stress granules in response to arsenic treatment. Interestingly, hYVH1-positive stress granules were significantly smaller, whereas knocking down hYVH1 expression attenuated stress granule breakdown during recovery from arsenite stress, indicating a possible role for hYVH1 in stress granule disassembly. These results propagate a role for dual specificity phosphatases at RNP particles and suggest that hYVH1 may affect a variety of fundamental cellular processes by regulating messenger ribonucleoprotein (mRNP) dynamics.
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Affiliation(s)
- Qiudi Geng
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Besa Xhabija
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Colleen Knuckle
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Christopher A Bonham
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Panayiotis O Vacratsis
- From the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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Ray A, Rana S, Banerjee D, Mitra A, Datta R, Naskar S, Sarkar S. Improved bioavailability of targeted Curcumin delivery efficiently regressed cardiac hypertrophy by modulating apoptotic load within cardiac microenvironment. Toxicol Appl Pharmacol 2015; 290:54-65. [PMID: 26612707 DOI: 10.1016/j.taap.2015.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 01/30/2023]
Abstract
Cardiomyocyte apoptosis acts as a prime modulator of cardiac hypertrophy leading to heart failure, a major cause of human mortality worldwide. Recent therapeutic interventions have focussed on translational applications of diverse pharmaceutical regimes among which, Curcumin (from Curcuma longa) is known to have an anti-hypertrophic potential but with limited pharmacological efficacies due to low aqueous solubility and poor bioavailability. In this study, Curcumin encapsulated by carboxymethyl chitosan (CMC) nanoparticle conjugated to a myocyte specific homing peptide was successfully delivered in bioactive form to pathological myocardium for effective regression of cardiac hypertrophy in a rat (Rattus norvegicus) model. Targeted nanotization showed higher cardiac bioavailability of Curcumin at a low dose of 5 mg/kg body weight compared to free Curcumin at 35 mg/kg body weight. Moreover, Curcumin/CMC-peptide treatment during hypertrophy significantly improved cardiac function by downregulating expression of hypertrophy marker genes (ANF, β-MHC), apoptotic mediators (Bax, Cytochrome-c) and activity of apoptotic markers (Caspase 3 and PARP); whereas free Curcumin in much higher dose showed minimal improvement during compromised cardiac function. Targeted Curcumin treatment significantly lowered p53 expression and activation in diseased myocardium via inhibited interaction of p53 with p300-HAT. Thus attenuated acetylation of p53 facilitated p53 ubiquitination and reduced the apoptotic load in hypertrophied cardiomyocytes; thereby limiting cardiomyocytes' need to enter the regeneration cycle during hypertrophy. This study elucidates for the first time an efficient targeted delivery regimen for Curcumin and also attributes towards probable mechanistic insight into its therapeutic potential as a cardio-protective agent for regression of cardiac hypertrophy.
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Affiliation(s)
- Aramita Ray
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, West Bengal, India.
| | - Santanu Rana
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, West Bengal, India.
| | - Durba Banerjee
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, West Bengal, India.
| | - Arkadeep Mitra
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, West Bengal, India.
| | - Ritwik Datta
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, West Bengal, India.
| | - Shaon Naskar
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, West Bengal, India.
| | - Sagartirtha Sarkar
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, West Bengal, India.
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Datta R, Bansal T, Rana S, Datta K, Chattopadhyay S, Chawla-Sarkar M, Sarkar S. Hsp90/Cdc37 assembly modulates TGFβ receptor-II to act as a profibrotic regulator of TGFβ signaling during cardiac hypertrophy. Cell Signal 2015; 27:2410-24. [PMID: 26362850 DOI: 10.1016/j.cellsig.2015.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/28/2015] [Accepted: 09/07/2015] [Indexed: 12/18/2022]
Abstract
Cardiac hypertrophy is accompanied by excessive collagen deposition in the heart. Despite painstaking research on this fatal disease, the precise role of molecular chaperones in myocardial fibrosis has not yet been elucidated. In this study, we have analyzed the mechanism by which Heat shock protein 90 (Hsp90)/Cell division cycle 37 (Cdc37) assembly modulates cardiac hypertrophy associated fibrosis. For the in vitro hypertrophy model, Angiotensin II (AngII) treated cultured adult cardiac fibroblasts were used, whereas the in vivo hypertrophy model was generated by renal artery ligation in adult male Wistar rats (Rattus norvegicus). Pretreatment with the Hsp90 inhibitor or the blocking of Hsp90-Cdc37 interactions during pressure overload hypertrophy resulted in ubiquitin-mediated proteasomal degradation of TGFβ receptor-II (TβR-II) leading to termination of TGFβ mediated signaling. In both cases significant reduction in collagen synthesis was observed revealing the Hsp90/Cdc37 complex as an integral profibrotic component of TGFβ signaling during cardiac hypertrophy.
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Affiliation(s)
- Ritwik Datta
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700 019, India.
| | - Trisha Bansal
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700 019, India.
| | - Santanu Rana
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700 019, India.
| | - Kaberi Datta
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700 019, India.
| | - Shiladitya Chattopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road Scheme-XM, Beliaghata, Kolkata-700010, India.
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road Scheme-XM, Beliaghata, Kolkata-700010, India.
| | - Sagartirtha Sarkar
- Genetics and Molecular Cardiology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata-700 019, India.
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Kim JA, Choi HK, Kim TM, Leem SH, Oh IH. Regulation of mesenchymal stromal cells through fine tuning of canonical Wnt signaling. Stem Cell Res 2015; 14:356-68. [PMID: 25863444 DOI: 10.1016/j.scr.2015.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023] Open
Abstract
Mesenchymal stromal cells (MSCs) have been extensively utilized for various cell therapeutic trials, but the signals regulating their stromal function remain largely unclear. Here, we show that canonical Wnt signals distinctively regulate MSCs in a biphasic manner depending on signal intensity, i.e., MSCs exhibit proliferation and progenitor self-renewal under low Wnt/β-catenin signaling, whereas they exhibit enhanced osteogenic differentiation with priming to osteoblast-like lineages under high Wnt/β-catenin signaling. Moreover, low or high levels of β-catenin in MSCs distinctly regulated the hematopoietic support of MSCs to promote proliferation or the undifferentiated state of hematopoietic progenitors, respectively. A gene expression study demonstrated that different intracellular levels of β-catenin in MSCs induce distinct transcriptomic changes in subsets of genes belonging to different gene function categories. Different β-catenin levels also induced differences in intracellular levels of the β-catenin co-factors, Tcf-1 and Lef-1. Moreover, nano-scale mass spectrometry of proteins that co-precipitated with β-catenin revealed distinctive spectra of proteins selectively interacting with β-catenin at specific expression levels. Together, these results show that Wnt/β-catenin signals can coax distinct transcription milieu to induce different transcription profiles in MSCs depending on the signal intensity and that fine-tuning of the canonical Wnt signaling intensity can regulate the phase-specific functionality of MSCs.
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Affiliation(s)
- Jin-A Kim
- Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, Republic of Korea
| | - Hyun-Kyung Choi
- Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, Republic of Korea
| | - Tae-Min Kim
- Center for Cancer Evolution, Medical Research Center, The Catholic University of Korea, Republic of Korea
| | - Sun-Hee Leem
- Dept. of Biological Science, Dong-A University, Busan, Republic of Korea
| | - Il-Hoan Oh
- Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, Republic of Korea.
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39
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Myeloid-derived growth factor (C19orf10) mediates cardiac repair following myocardial infarction. Nat Med 2015; 21:140-9. [PMID: 25581518 DOI: 10.1038/nm.3778] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/21/2014] [Indexed: 01/20/2023]
Abstract
Paracrine-acting proteins are emerging as a central mechanism by which bone marrow cell-based therapies improve tissue repair and heart function after myocardial infarction (MI). We carried out a bioinformatic secretome analysis in bone marrow cells from patients with acute MI to identify novel secreted proteins with therapeutic potential. Functional screens revealed a secreted protein encoded by an open reading frame on chromosome 19 (C19orf10) that promotes cardiac myocyte survival and angiogenesis. We show that bone marrow-derived monocytes and macrophages produce this protein endogenously to protect and repair the heart after MI, and we named it myeloid-derived growth factor (MYDGF). Whereas Mydgf-deficient mice develop larger infarct scars and more severe contractile dysfunction compared to wild-type mice, treatment with recombinant Mydgf reduces scar size and contractile dysfunction after MI. This study is the first to assign a biological function to MYDGF, and it may serve as a prototypical example for the development of protein-based therapies for ischemic tissue repair.
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40
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Borner GHH, Hein MY, Hirst J, Edgar JR, Mann M, Robinson MS. Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol Biol Cell 2014; 25:3178-94. [PMID: 25165137 PMCID: PMC4196868 DOI: 10.1091/mbc.e14-07-1198] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 01/06/2023] Open
Abstract
We developed "fractionation profiling," a method for rapid proteomic analysis of membrane vesicles and protein particles. The approach combines quantitative proteomics with subcellular fractionation to generate signature protein abundance distribution profiles. Functionally associated groups of proteins are revealed through cluster analysis. To validate the method, we first profiled >3500 proteins from HeLa cells and identified known clathrin-coated vesicle proteins with >90% accuracy. We then profiled >2400 proteins from Drosophila S2 cells, and we report the first comprehensive insect clathrin-coated vesicle proteome. Of importance, the cluster analysis extends to all profiled proteins and thus identifies a diverse range of known and novel cytosolic and membrane-associated protein complexes. We show that it also allows the detailed compositional characterization of complexes, including the delineation of subcomplexes and subunit stoichiometry. Our predictions are presented in an interactive database. Fractionation profiling is a universal method for defining the clathrin-coated vesicle proteome and may be adapted for the analysis of other types of vesicles and particles. In addition, it provides a versatile tool for the rapid generation of large-scale protein interaction maps.
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Affiliation(s)
- Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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41
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Al-Majdoub M, Opuni KFM, Yefremova Y, Koy C, Lorenz P, El-Kased RF, Thiesen HJ, Glocker MO. A novel strategy for the rapid preparation and isolation of intact immune complexes from peptide mixtures. J Mol Recognit 2014; 27:566-74. [DOI: 10.1002/jmr.2375] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/27/2014] [Accepted: 03/13/2014] [Indexed: 01/10/2023]
Affiliation(s)
| | | | - Yelena Yefremova
- Proteome Center Rostock; University Medicine Rostock; Rostock Germany
| | - Cornelia Koy
- Proteome Center Rostock; University Medicine Rostock; Rostock Germany
| | - Peter Lorenz
- Institute of Immunology; University Medicine Rostock; Rostock Germany
| | - Reham F. El-Kased
- Microbiology and Immunology Faculty of Pharmacy; The British University in Egypt; Cairo Egypt
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42
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Hirst J, Schlacht A, Norcott JP, Traynor D, Bloomfield G, Antrobus R, Kay RR, Dacks JB, Robinson MS. Characterization of TSET, an ancient and widespread membrane trafficking complex. eLife 2014; 3:e02866. [PMID: 24867644 PMCID: PMC4031984 DOI: 10.7554/elife.02866] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/14/2014] [Indexed: 12/31/2022] Open
Abstract
The heterotetrameric AP and F-COPI complexes help to define the cellular map of modern eukaryotes. To search for related machinery, we developed a structure-based bioinformatics tool, and identified the core subunits of TSET, a 'missing link' between the APs and COPI. Studies in Dictyostelium indicate that TSET is a heterohexamer, with two associated scaffolding proteins. TSET is non-essential in Dictyostelium, but may act in plasma membrane turnover, and is essentially identical to the recently described TPLATE complex, TPC. However, whereas TPC was reported to be plant-specific, we can identify a full or partial complex in every eukaryotic supergroup. An evolutionary path can be deduced from the earliest origins of the heterotetramer/scaffold coat to its multiple manifestations in modern organisms, including the mammalian muniscins, descendants of the TSET medium subunits. Thus, we have uncovered the machinery for an ancient and widespread pathway, which provides new insights into early eukaryotic evolution.DOI: http://dx.doi.org/10.7554/eLife.02866.001.
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Affiliation(s)
- Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | | | - John P Norcott
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - David Traynor
- Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Gareth Bloomfield
- Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Robert R Kay
- Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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Shimazaki Y, Nishimura Y, Saito M. Antigen digestion on the target plate of MALDI-TOF MS after isolation using an immunoaffinity membrane. J Pharm Biomed Anal 2013; 83:293-8. [DOI: 10.1016/j.jpba.2013.05.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/18/2013] [Accepted: 05/21/2013] [Indexed: 10/26/2022]
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Hirst J, Borner GHH, Edgar J, Hein MY, Mann M, Buchholz F, Antrobus R, Robinson MS. Interaction between AP-5 and the hereditary spastic paraplegia proteins SPG11 and SPG15. Mol Biol Cell 2013; 24:2558-69. [PMID: 23825025 PMCID: PMC3744948 DOI: 10.1091/mbc.e13-03-0170] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The AP-5 complex is a recently identified but evolutionarily ancient member of the family of heterotetrameric adaptor proteins (AP complexes). It is associated with two proteins that are mutated in patients with hereditary spastic paraplegia, SPG11 and SPG15. Here we show that the four AP-5 subunits can be coimmunoprecipitated with SPG11 and SPG15, both from cytosol and from detergent-extracted membranes, with a stoichiometry of ∼1:1:1:1:1:1. Knockdowns of SPG11 or SPG15 phenocopy knockdowns of AP-5 subunits: all six knockdowns cause the cation-independent mannose 6-phosphate receptor to become trapped in clusters of early endosomes. In addition, AP-5, SPG11, and SPG15 colocalize on a late endosomal/lysosomal compartment. Both SPG11 and SPG15 have predicted secondary structures containing α-solenoids related to those of clathrin heavy chain and COPI subunits. SPG11 also has an N-terminal, β-propeller-like domain, which interacts in vitro with AP-5. We propose that AP-5, SPG15, and SPG11 form a coat-like complex, with AP-5 involved in protein sorting, SPG15 facilitating the docking of the coat onto membranes by interacting with PI3P via its FYVE domain, and SPG11 (possibly together with SPG15) forming a scaffold.
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Affiliation(s)
- Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom.
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Mitra A, Basak T, Datta K, Naskar S, Sengupta S, Sarkar S. Role of α-crystallin B as a regulatory switch in modulating cardiomyocyte apoptosis by mitochondria or endoplasmic reticulum during cardiac hypertrophy and myocardial infarction. Cell Death Dis 2013; 4:e582. [PMID: 23559016 PMCID: PMC3641337 DOI: 10.1038/cddis.2013.114] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cardiac hypertrophy and myocardial infarction (MI) are two major causes of heart failure with different etiologies. However, the molecular mechanisms associated with these two diseases are not yet fully understood. So, this study was designed to decipher the process of cardiomyocyte apoptosis during cardiac hypertrophy and MI in vivo. Our study revealed that mitochondrial outer membrane channel protein voltage-dependent anion channel-1 (VDAC1) was upregulated exclusively during cardiac hypertrophy, whereas 78 kDa glucose-regulated protein (GRP78) was exclusively upregulated during MI, which is an important upstream regulator of the endoplasmic reticulum (ER) stress pathway. Further downstream analysis revealed that mitochondrial pathway of apoptosis is instrumental in case of hypertrophy, whereas ER stress-induced apoptosis is predominant during MI, which was confirmed by treatment with either siRNA against VDAC1 or ER stress inhibitor tauroursodeoxycholic acid (TUDCA). Very interestingly, our data also showed that the expression and interaction of small heat-shock protein α-crystallin B (CRYAB) with VDAC1 was much more pronounced during MI compared with either hypertrophy or control. The study demonstrated for the first time that two different organelles—mitochondria and ER have predominant roles in mediating cardiomyocyte death signaling during hypertrophy and MI, respectively, and activation of CRYAB acts as a molecular switch in bypassing mitochondrial pathway of apoptosis during MI.
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Affiliation(s)
- A Mitra
- Department of Zoology, University of Calcutta, 35, B.C. Road, Kolkata 700 019, India
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Miteva YV, Budayeva HG, Cristea IM. Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem 2013; 85:749-68. [PMID: 23157382 PMCID: PMC3666915 DOI: 10.1021/ac3033257] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Ileana M. Cristea
- Corresponding author: Ileana M. Cristea 210 Lewis Thomas Laboratory Department of Molecular Biology Princeton University Princeton, NJ 08544 Tel: 6092589417 Fax: 6092584575
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Borner GHH, Antrobus R, Hirst J, Bhumbra GS, Kozik P, Jackson LP, Sahlender DA, Robinson MS. Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles. ACTA ACUST UNITED AC 2012; 197:141-60. [PMID: 22472443 PMCID: PMC3317806 DOI: 10.1083/jcb.201111049] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A multivariate proteomics approach identified numerous new clathrin-coated vesicle proteins as well as the first AP-4 accessory protein, and also revealed how auxilin depletion causes mitotic arrest through sequestration of spindle proteins in clathrin cages. Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions.
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Affiliation(s)
- Georg H H Borner
- Cambridge Institute for Medical Research, Wellcome Trust/Medical Research Council Building, University of Cambridge, Cambridge CB2 0XY, England, UK.
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Cj1386 is an ankyrin-containing protein involved in heme trafficking to catalase in Campylobacter jejuni. J Bacteriol 2011; 194:334-45. [PMID: 22081390 DOI: 10.1128/jb.05740-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Campylobacter jejuni, a microaerophilic bacterium, is the most frequent cause of human bacterial gastroenteritis. C. jejuni is exposed to harmful reactive oxygen species (ROS) produced during its own normal metabolic processes and during infection from the host immune system and from host intestinal microbiota. These ROS will damage DNA and proteins and cause peroxidation of lipids. Consequently, identifying ROS defense mechanisms is important for understanding how Campylobacter survives this environmental stress during infection. Construction of a ΔCj1386 isogenic deletion mutant and phenotypic assays led to its discovery as a novel oxidative stress defense gene. The ΔCj1386 mutant has an increased sensitivity toward hydrogen peroxide. The Cj1386 gene is located directly downstream from katA (catalase) in the C. jejuni genome. A ΔkatAΔ Cj1386 double deletion mutant was constructed and exhibited a sensitivity to hydrogen peroxide similar to that seen in the ΔCj1386 and ΔkatA single deletion mutants. This observation suggests that Cj1386 may be involved in the same detoxification pathway as catalase. Despite identical KatA abundances, catalase activity assays showed that the ΔCj1386 mutant had a reduced catalase activity relative to that of wild-type C. jejuni. Heme quantification of KatA protein from the ΔCj1386 mutant revealed a significant decrease in heme concentration. This indicates an important role for Cj1386 in heme trafficking to KatA within C. jejuni. Interestingly, the ΔCj1386 mutant had a reduced ability to colonize the ceca of chicks and was outcompeted by the wild-type strain for colonization of the gastrointestinal tract of neonate piglets. These results indicate an important role for Cj1386 in Campylobacter colonization and pathogenesis.
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Ju F, Zhao Y, Zhao Y, Wang Y, Wen F, Ye L, Gao L. Interaction between Pax6 and its novel mutant in Bufo raddei Strauch. Mol Vis 2011; 17:2698-705. [PMID: 22065923 PMCID: PMC3209426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/06/2011] [Indexed: 11/02/2022] Open
Abstract
PURPOSE Exploration of the relationship between a novel paired box 6 (Pax6) mutant and Pax6 in Bufo raddei Strauch. METHODS RT-PCR, yeast 2-hybrid system, and co-immunoprecipitation were used to analyze the Pax6 protein and its mutant during embryonic eye development in Bufo raddei Strauch. RESULTS We have cloned the Pax6 ORF sequence from Bufo raddei Strauch. Here we report the cloning of a novel Pax6 homolog of Bufo raddei Strauch named Pax6 variant. Comparing the 2 genes, the homolog of ORF nucleotide sequence is more than 99% in Bufo raddei Strauch; only the proline-serine-threonine(PST)-rich transaction domain differs. The deduced amino acid sequences of PST region are 53.1% identical. An interaction was found between Pax6 and Pax6 variant via yeast 2-hybrid system; with further study, we found that they interacted in vivo via co-immunopricipitation. CONCLUSIONS A Pax6 mutant was first found in Bufo raddei Strauch. Interaction between Pax6 and Pax6 variant may play a critical role during eye development in Bufo raddei Strauch. This suggests that expression of Pax6 variant may play a role and appears to be a necessity in eye development, but that Pax6 itself is still pivotal in eye development.
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Affiliation(s)
- Furong Ju
- School of Life Science, Lanzhou University, Gansu, China
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